Annual reports show Otago and Canterbury universities recorded deficits last year.
However, Auckland's AUT reported a surplus despite a drop in enrolments.
AUT's 2023 annual report said its full-time student numbers dropped slightly to 18,724 due to falling domestic student numbers.
"Domestic enrolments fell more than 6 percent from 2022, driven by both a softening of the school leaver market and lower retention rates for current students... the impact was partially offset by the better-than expected recovery in the international market - we had over 700 more international students than anticipated for the year," the report said.
It said AUT made a surplus of $9.7 million last year.
The University of Otago reported a small fall in full-time student numbers to 18,960.
"Reasons for this were varied, but can be largely traced back to the global COVID-19 pandemic, and included a smaller Year 13 school leaver cohort and a reduced flow from that cohort on to tertiary study; an unanticipated drop in student retention from 2022 to 2023; and rapid increases in the cost of living which caused students to either pause their studies or lighten their loads considerably in order to accommodate paid work," Otago's annual report said.
The report said Otago had to cut spending by $60m last year, prompting 216 voluntary and forced redundancies.
It said the university made a deficit of $360,000 and had budgeted for a further deficit in 2024.
The University of Canterbury's annual report said its full-time student count rose to more than 17,187, its highest-ever total.
The report showed the university's income exceeded $500m for the first time, however it made a $14m deficit last year and it was expecting a further deficit in 2024.
"The university has adopted a group budget for 2024 that shows an operating deficit of $19.6 million, which represents the continued investment by the university to support strong digital foundations, innovative new programmes and course delivery, and increasing financial sustainability," Canterbury's annual report said.
The university's executive director of planning, finance and digital services, Keith Longden, told RNZ the university was investing in projects that would lead to long-term growth or future savings.
The university expected to make a surplus in 2026 and in the meantime cashflow was strong, enrolments had continued to grow this year and it was in a sound financial position, he said.
"As can be seen in our latest annual report, the university has cash reserves of $233m and no debt," he said.